Contacts of the helix formed by residues 324 - 331 (chain A) in PDB entry 2OXD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.3 29.8 - - - -
137A ILE* 3.7 7.4 - - + -
138A TYR* 3.7 33.0 - + + -
141A LEU* 3.6 13.7 - - + -
300A PHE* 3.5 32.1 - + - -
318A ALA 3.1 29.6 - - - -
319A MET* 3.9 3.1 - - - +
321A HIS* 2.7 17.8 + - + +
323A TYR* 1.3 99.6 - + - +
325A GLN* 1.3 55.1 + - - +
326A GLN 3.3 2.7 - - - -
327A VAL* 2.8 29.0 + - + +
328A ARG* 3.0 20.9 + - - +
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Residues in contact with GLN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 6.1 0.6 - - - +
296A GLU* 6.0 1.6 - - - +
321A HIS 3.9 1.0 + - - -
322A PRO* 3.1 28.6 + - + +
323A TYR 3.3 1.4 - - - -
324A PHE* 1.3 76.2 - - - +
326A GLN* 1.3 62.6 + - + +
328A ARG* 3.4 25.5 + - - +
329A ALA* 3.0 29.9 + - + +
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP* 5.8 1.6 + - - -
131A TYR* 3.8 32.4 + - + +
134A ARG* 5.4 14.9 - - - +
323A TYR 5.0 0.8 + - - +
324A PHE 3.3 0.8 - - - -
325A GLN* 1.3 83.6 - - + +
327A VAL* 1.3 58.3 + - + +
329A ALA* 3.5 8.0 + - + +
330A ALA* 3.1 26.7 + - - +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR* 3.7 24.2 - - + +
134A ARG* 3.8 30.1 - - + +
135A TYR* 3.8 28.9 - - + +
138A TYR* 3.7 36.3 - - + -
139A GLU* 5.0 0.7 - - - +
324A PHE* 2.8 15.8 + - + +
326A GLN* 1.3 74.7 - - + +
328A ARG* 1.3 63.4 + - - +
330A ALA* 3.4 4.5 + - - +
331A GLU* 3.2 22.1 + - - +
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Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 3.5 27.8 - - + +
319A MET 2.9 22.8 + - - -
320A THR* 3.1 25.2 + - - +
321A HIS 2.8 26.2 + - - -
322A PRO* 4.1 5.3 - - - +
324A PHE* 3.0 14.7 + - - +
325A GLN* 3.5 30.1 + - - +
327A VAL* 1.3 74.2 - - - +
329A ALA* 1.3 62.2 + - - +
331A GLU* 3.3 25.0 + - - +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A GLN* 3.0 18.6 + - + +
326A GLN* 3.6 10.5 - - + +
327A VAL 3.2 0.2 - - - -
328A ARG* 1.3 74.7 - - - +
330A ALA* 1.3 64.9 + - - +
331A GLU 3.1 8.5 - - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR* 3.5 24.9 - - - +
326A GLN 3.1 10.0 + - - +
327A VAL 3.7 3.8 - - - +
328A ARG 3.4 0.2 - - - -
329A ALA* 1.3 76.4 - - - +
331A GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 3.5 18.8 + - - -
139A GLU* 4.6 1.7 - - - +
142A LYS* 2.7 39.3 + - - -
327A VAL* 3.2 14.1 + - - +
328A ARG* 3.3 14.8 - - - +
329A ALA 3.1 10.8 - - - +
330A ALA* 1.3 83.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il